Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 53 of 150
Found at i:15790391 original size:11 final size:11
Alignment explanation
Indices: 15790370--15790414 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
15790360 ATAGTAGTTT
15790370 CTCGAAAAAAAA
1 CTCG-AAAAAAA
15790382 CTCGAAAAAAA
1 CTCGAAAAAAA
* *
15790393 ATCAAAAAAAA
1 CTCGAAAAAAA
*
15790404 TTCGAAAAAAA
1 CTCGAAAAAAA
15790415 ACTAGTTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.69, C:0.13, G:0.07, T:0.11
Consensus pattern (11 bp):
CTCGAAAAAAA
Found at i:15790402 original size:22 final size:22
Alignment explanation
Indices: 15790374--15790415 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
15790364 TAGTTTCTCG
15790374 AAAAAAAACTCGAAAAAAAATC
1 AAAAAAAACTCGAAAAAAAATC
*
15790396 AAAAAAAATTCGAAAAAAAA
1 AAAAAAAACTCGAAAAAAAA
15790416 CTAGTTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.10, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAAAAAACTCGAAAAAAAATC
Found at i:15790475 original size:14 final size:14
Alignment explanation
Indices: 15790453--15790493 Score: 66
Period size: 13 Copynumber: 3.0 Consensus size: 14
15790443 GGATATCAAG
15790453 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
15790467 TTTTG-AAAAAAAA
1 TTGTGAAAAAAAAA
15790480 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
15790494 AGAGAGCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:15797505 original size:20 final size:20
Alignment explanation
Indices: 15797472--15797548 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
15797462 TGTAGAACAA
*
15797472 AGGCACCAAAGTGCAAATAG
1 AGGCATCAAAGTGCAAATAG
* *
15797492 AGGCATGAATGTGC-AATCAG
1 AGGCATCAAAGTGCAAAT-AG
*
15797512 AGGCACCAAAGTGCAAATAG
1 AGGCATCAAAGTGCAAATAG
15797532 AGGCATCAAAGTGCAAA
1 AGGCATCAAAGTGCAAA
15797549 CCCATACAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.43, C:0.18, G:0.26, T:0.13
Consensus pattern (20 bp):
AGGCATCAAAGTGCAAATAG
Found at i:15797517 original size:40 final size:40
Alignment explanation
Indices: 15797472--15797547 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
15797462 TGTAGAACAA
* *
15797472 AGGCACCAAAGTGCAAATAGAGGCATGAATGTGCAATCAG
1 AGGCACCAAAGTGCAAATAGAGGCATCAAAGTGCAATCAG
15797512 AGGCACCAAAGTGCAAATAGAGGCATCAAAGTGCAA
1 AGGCACCAAAGTGCAAATAGAGGCATCAAAGTGCAA
15797548 ACCCATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.13
Consensus pattern (40 bp):
AGGCACCAAAGTGCAAATAGAGGCATCAAAGTGCAATCAG
Found at i:15809319 original size:15 final size:18
Alignment explanation
Indices: 15809299--15809336 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
15809289 CTGTCAATCT
15809299 TTTTCTTTT-TCA-TC-C
1 TTTTCTTTTCTCACTCTC
15809314 TTTTCTTTTCTCACTCTC
1 TTTTCTTTTCTCACTCTC
15809332 TTTTC
1 TTTTC
15809337 ACTCTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 2 0.10
18 6 0.30
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTCTTTTCTCACTCTC
Found at i:15816472 original size:12 final size:10
Alignment explanation
Indices: 15816443--15816482 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
15816433 TCAAAAATAG
15816443 TTAAAATTAA
1 TTAAAATTAA
*
15816453 TCAAAATTAA
1 TTAAAATTAA
15816463 CTATAAAATTAA
1 -T-TAAAATTAA
15816475 TTAAAATT
1 TTAAAATT
15816483 CATCATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATTAA
Found at i:15828269 original size:42 final size:42
Alignment explanation
Indices: 15828171--15828279 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
15828161 ATGTCCTACC
* * * *
15828171 ACACGGCCTGGCACACGGGCATGTGAGGCTACTTTGAAGGGT
1 ACACGACCTGGCACATGGGCGTGTGAGGCTACTTCGAAGGGT
* *
15828213 ACACGGCCAT-GCACATGGGTGTGTGAGGCTACTTCGAAGGGT
1 ACACGACC-TGGCACATGGGCGTGTGAGGCTACTTCGAAGGGT
* * *
15828255 ACACTATCTGGCACATAGGCGTGTG
1 ACACGACCTGGCACATGGGCGTGTG
15828280 GCTTGGCCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 54 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (42 bp):
ACACGACCTGGCACATGGGCGTGTGAGGCTACTTCGAAGGGT
Found at i:15839501 original size:6 final size:6
Alignment explanation
Indices: 15839478--15839537 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
15839468 TTTTAAGAAA
* * * *
15839478 ATTTAT ATTTTT AGTTTT ATTTTT CTTTTT CATTTTT ATCTTT ACTTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT -ATTTTT ATTTTT A-TTTTT
15839528 ATTTTT ATTT
1 ATTTTT ATTT
15839538 AATTTGTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 35 0.78
7 10 0.22
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:15839507 original size:19 final size:18
Alignment explanation
Indices: 15839485--15839537 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
15839475 AAAATTTATA
* *
15839485 TTTTTAGTTTTATTTTTC
1 TTTTTATTTTTATTTTAC
15839503 TTTTTCATTTTTATCTTTAC
1 TTTTT-ATTTTTAT-TTTAC
15839523 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
15839538 AATTTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.23
19 15 0.48
20 9 0.29
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTATTTTTATTTTAC
Found at i:15841702 original size:25 final size:25
Alignment explanation
Indices: 15841668--15841717 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
15841658 AAAGGAGGGG
*
15841668 TAAGGCATTTCACCTGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
15841693 TAAGGCATTTCACATGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
15841718 AGTATGTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (25 bp):
TAAGGCATTTCACATGAATTTTTAA
Found at i:15844735 original size:20 final size:20
Alignment explanation
Indices: 15844710--15844756 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
15844700 AGCTCGTTTC
*
15844710 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
15844730 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
15844750 CAGCTCA
1 CAGCTCA
15844757 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:15847011 original size:37 final size:38
Alignment explanation
Indices: 15846927--15847013 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
15846917 AGAAAATGAC
* *
15846927 TAAAGAACAAAGAAAAGTTTGCTCAAATTCTAGAAAAAA
1 TAAAGAGCAAAGAAAAGATTGCTCAAATTCTA-AAAAAA
*
15846966 TAAA-AGCAAATAAAAGATTGCTCAAATTCT-AAAAAA
1 TAAAGAGCAAAGAAAAGATTGCTCAAATTCTAAAAAAA
15847002 TAAAGAGCAAAG
1 TAAAGAGCAAAG
15847014 TTTGCTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 10 0.23
37 6 0.14
38 23 0.53
39 4 0.09
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (38 bp):
TAAAGAGCAAAGAAAAGATTGCTCAAATTCTAAAAAAA
Found at i:15847053 original size:38 final size:35
Alignment explanation
Indices: 15846940--15847055 Score: 112
Period size: 38 Copynumber: 3.2 Consensus size: 35
15846930 AGAACAAAGA
* **
15846940 AAAGTTTGCTCAAATTCTAGAAAAAATAAAAGCAAATA
1 AAAGTTTGCTCAAATTCTA-AAAAAATAAAAG--GAGC
*
15846978 AAAGATTGCTCAAATTCT-AAAAAAT-AAA-GAGC
1 AAAGTTTGCTCAAATTCTAAAAAAATAAAAGGAGC
*
15847010 AAAGTTTGCTCAAAGTCTAAAAAAATAAAAGTTGAGC
1 AAAGTTTGCTCAAATTCTAAAAAAATAAAAG--GAGC
15847047 ATAAGTTTG
1 A-AAGTTTG
15847056 ACATAAGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
32 17 0.26
33 7 0.11
34 3 0.05
35 3 0.05
36 7 0.11
37 5 0.08
38 24 0.36
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (35 bp):
AAAGTTTGCTCAAATTCTAAAAAAATAAAAGGAGC
Found at i:15854967 original size:30 final size:30
Alignment explanation
Indices: 15854833--15854967 Score: 103
Period size: 30 Copynumber: 4.5 Consensus size: 30
15854823 AGAAGCTATC
* * *
15854833 ATGGTCGTCACCATCCCTTATCATTGTTTG
1 ATGGTTGTCACCATCCCTTTTCATAGTTTG
* *
15854863 ATGGGTGTCACCATCCCTTTTCATAATTTG
1 ATGGTTGTCACCATCCCTTTTCATAGTTTG
* * * * * **
15854893 ATAGCTG-AAGCTATCCCTTTTCATAGATCA
1 ATGGTTGTCA-CCATCCCTTTTCATAGTTTG
* * *
15854923 ATAGTCG-AAGCCATCCCTTTTCATAGTTTG
1 ATGGTTGTCA-CCATCCCTTTTCATAGTTTG
15854953 ATGGTTGTCACCATC
1 ATGGTTGTCACCATC
15854968 ATTTGAAGAA
Statistics
Matches: 81, Mismatches: 22, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
29 1 0.01
30 79 0.98
31 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (30 bp):
ATGGTTGTCACCATCCCTTTTCATAGTTTG
Found at i:15862105 original size:30 final size:30
Alignment explanation
Indices: 15862060--15862223 Score: 138
Period size: 30 Copynumber: 5.5 Consensus size: 30
15862050 AGCTGAAGCT
* *
15862060 ATCCCTTTCCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * * *
15862090 ATCCATTTTCATAATTCGATAGTCG--GCT
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* *** *
15862118 ATCCCTTTTCATAGA-TCAATAACCG-AAGCC
1 ATCCCTTTTCATA-ATTCGATGGTCGTCA-CC
* *
15862148 ATCCCATTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *
15862178 ATCCCTTTTCATAATTTGATGTTAGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
15862208 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
15862224 TATAACCAAA
Statistics
Matches: 105, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
28 20 0.19
29 1 0.01
30 83 0.79
31 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGGTCGTCACC
Found at i:15862146 original size:88 final size:87
Alignment explanation
Indices: 15862029--15862244 Score: 238
Period size: 88 Copynumber: 2.4 Consensus size: 87
15862019 TGACCAAAGT
* * * * * *
15862029 TATCCCTTTTGATAGTTCGATAGCTGAAGCTATCCCTTTCCATAATTTGATGGTCGTCACCATCC
1 TATCCCTTTTCATAGATCAATAACCGAAGCTATCCCTTT-CATAATTCGATGGTCGTCACCATCC
*
15862094 ATTTTCATAATTCGA-TAGTCGGC
65 ATTTTCATAATTCGATTAGTC-AC
* *
15862117 TATCCCTTTTCATAGATCAATAACCGAAGCCATCCCATTTCATAGTTCGATGGTCGTCACCATCC
1 TATCCCTTTTCATAGATCAATAACCGAAGCTATCCC-TTTCATAATTCGATGGTCGTCACCATCC
* *
15862182 CTTTTCATAATTTGATGTTAGTCAC
65 ATTTTCATAATTCGA--TTAGTCAC
* ** *
15862207 CATCCCTTTTCATA-ATTTATAACCAAAGCTATCCCTTT
1 TATCCCTTTTCATAGATCAATAACCGAAGCTATCCCTTT
15862245 TCTTATTCGA
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
88 69 0.64
89 20 0.19
90 14 0.13
91 5 0.05
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (87 bp):
TATCCCTTTTCATAGATCAATAACCGAAGCTATCCCTTTCATAATTCGATGGTCGTCACCATCCA
TTTTCATAATTCGATTAGTCAC
Found at i:15865807 original size:36 final size:36
Alignment explanation
Indices: 15865719--15865838 Score: 123
Period size: 36 Copynumber: 3.3 Consensus size: 36
15865709 CGTCAGTCCA
* * *
15865719 ACCAAAACACAGCAGATGGTCACATGAGCTAATCCC
1 ACCAAAACACACCAGATGCTCACATGAGCCAATCCC
*** * *
15865755 TGTAAGACACAACAGATGCTCACATGAGCCAATCCC
1 ACCAAAACACACCAGATGCTCACATGAGCCAATCCC
* * *
15865791 ACCAAAATACACCAGATGCTCACACGAGCCAATCGC
1 ACCAAAACACACCAGATGCTCACATGAGCCAATCCC
* *
15865827 TCCAAAATACAC
1 ACCAAAACACAC
15865839 AAATGCTTAT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.14
Consensus pattern (36 bp):
ACCAAAACACACCAGATGCTCACATGAGCCAATCCC
Found at i:15867026 original size:204 final size:204
Alignment explanation
Indices: 15866655--15867058 Score: 745
Period size: 204 Copynumber: 2.0 Consensus size: 204
15866645 GCTAGTTGAA
*
15866655 CCTAGATGCAACGATCTCAAAAATATAAAAATTACAACAAATGAACATCAAAATTCATTTACATC
1 CCTAGATGCAACGATCTCAAAAATATAAAAATTACAACAAATGAACATCAAAATTCACTTACATC
*
15866720 CAATGAAAATAAGAAAACCAAATCTCCTTCACCCTAGCTATGTGGTGCGAACCTGGTCGCATCAT
66 CAATGAAAATAAGAAAACCAAATCTCCTTCACCCTAGCTATGTGGTACGAACCTGGTCGCATCAT
* *
15866785 GTTTCGATACATCTCGACGACATCGGGATTGGCCTAAACTTGAAGGGCCCAAGTGCAAGATGAAA
131 GTTTCGATACATCTCGACGACATCGGGATTAGCCTAAACTTGAAGAGCCCAAGTGCAAGATGAAA
15866850 CATCTTAAC
196 CATCTTAAC
* *
15866859 CCTAGCTGCAATGATCTCAAAAATATAAAAATTACAACAAATGAACATCAAAATTCACTTACATC
1 CCTAGATGCAACGATCTCAAAAATATAAAAATTACAACAAATGAACATCAAAATTCACTTACATC
15866924 CAATGAAAATAAGAAAACCAAATCTCCTTCACCCTAGCTATGTGGTACGAACCTGGTCGCATCAT
66 CAATGAAAATAAGAAAACCAAATCTCCTTCACCCTAGCTATGTGGTACGAACCTGGTCGCATCAT
*
15866989 GTTTCGATACATCTCGACGACATTGGGATTAGCCTAAACTTGAAGAGCCCAAGTGCAAGATGAAA
131 GTTTCGATACATCTCGACGACATCGGGATTAGCCTAAACTTGAAGAGCCCAAGTGCAAGATGAAA
15867054 CATCT
196 CATCT
15867059 CTTAGGCCTG
Statistics
Matches: 193, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
204 193 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (204 bp):
CCTAGATGCAACGATCTCAAAAATATAAAAATTACAACAAATGAACATCAAAATTCACTTACATC
CAATGAAAATAAGAAAACCAAATCTCCTTCACCCTAGCTATGTGGTACGAACCTGGTCGCATCAT
GTTTCGATACATCTCGACGACATCGGGATTAGCCTAAACTTGAAGAGCCCAAGTGCAAGATGAAA
CATCTTAAC
Found at i:15869571 original size:27 final size:27
Alignment explanation
Indices: 15869522--15869574 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
15869512 ATGTTGTAAT
*
15869522 GAAAAAGAAAAAGAGATTGAAAAAGAG
1 GAAAAAGAAAAAGAGATTAAAAAAGAG
15869549 GAAAAAGAAAAAGA-AGTTAAAAAAGA
1 GAAAAAGAAAAAGAGA-TTAAAAAAGA
15869575 AATTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.08
Consensus pattern (27 bp):
GAAAAAGAAAAAGAGATTAAAAAAGAG
Found at i:15869582 original size:39 final size:39
Alignment explanation
Indices: 15869529--15869603 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
15869519 AATGAAAAAG
* *
15869529 AAAAAGAGATTGAAAAAGAGGAAAAAGAAAAAGAAGTTA
1 AAAAAGAAATTGAAAAAGAAGAAAAAGAAAAAGAAGTTA
**
15869568 AAAAAGAAATTGAAAATTAAGAAAAAGAAAAAGAAG
1 AAAAAGAAATTGAAAAAGAAGAAAAAGAAAAAGAAG
15869604 AAAAAGAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (39 bp):
AAAAAGAAATTGAAAAAGAAGAAAAAGAAAAAGAAGTTA
Found at i:15869597 original size:15 final size:15
Alignment explanation
Indices: 15869586--15869617 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15869576 ATTGAAAATT
15869586 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
*
15869601 AAGAAAAAGAGAAAG
1 AAGAAAAAGAAAAAG
15869616 AA
1 AA
15869618 AATGATAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:15874824 original size:25 final size:25
Alignment explanation
Indices: 15874790--15874842 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
15874780 CACAACATAA
*
15874790 CTCGTATGAGCTTACTGATTTTTAG
1 CTCGTATGAGCTTACTAATTTTTAG
15874815 CTCGTATGAGCTTACTAATTTTTAG
1 CTCGTATGAGCTTACTAATTTTTAG
15874840 CTC
1 CTC
15874843 TTAAGAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (25 bp):
CTCGTATGAGCTTACTAATTTTTAG
Found at i:15874850 original size:25 final size:25
Alignment explanation
Indices: 15874790--15874850 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
15874780 CACAACATAA
* *
15874790 CTCGTATGAGCTTACTGATTTTTAG
1 CTCGTAAGAGCTTACTAATTTTTAG
*
15874815 CTCGTATGAGCTTACTAATTTTTAG
1 CTCGTAAGAGCTTACTAATTTTTAG
*
15874840 CTCTTAAGAGC
1 CTCGTAAGAGC
15874851 ATACCGATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (25 bp):
CTCGTAAGAGCTTACTAATTTTTAG
Found at i:15881473 original size:50 final size:50
Alignment explanation
Indices: 15881378--15881501 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
15881368 TATTGAGCTT
* * * *
15881378 ATGAGAGGCCCCACGTAAGACCATGTATGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTATGGGACATGACATGGGCACCGAG
* * * *
15881428 ATGAGAGGTCCCTCGTAAGACCATGTTTGGGACATGACATGGGCACTGAT
1 ATGAGAGGTCCCACGTAAGACCATGTATGGGACATGACATGGGCACCGAG
** *
15881478 ATGAGAATTCCCAAGTAAGACCAT
1 ATGAGAGGTCCCACGTAAGACCAT
15881502 ATCTGGGATA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTATGGGACATGACATGGGCACCGAG
Found at i:15883389 original size:49 final size:49
Alignment explanation
Indices: 15883283--15883406 Score: 160
Period size: 49 Copynumber: 2.5 Consensus size: 49
15883273 GTACATGTAT
* * * *
15883283 GCTCAAACGAGCTATGAATCGGTATGCTCTCACAAGCTGTAAATTGGTAA
1 GCTCATACGAGCTA-GAATCGGTAAGATCTCACAAGCTGAAAATTGGTAA
*
15883333 GCTCATACGAGCTGAGAATTGGTAAGATCTCACAAGCT-AAAATTGGTAA
1 GCTCATACGAGCT-AGAATCGGTAAGATCTCACAAGCTGAAAATTGGTAA
*
15883382 GCTCATACAAGCTAAGAATCGGTAA
1 GCTCATACGAGCT-AGAATCGGTAA
15883407 TCCCTGATGC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 32 0.49
50 32 0.49
51 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (49 bp):
GCTCATACGAGCTAGAATCGGTAAGATCTCACAAGCTGAAAATTGGTAA
Found at i:15883396 original size:24 final size:25
Alignment explanation
Indices: 15883314--15883394 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
15883304 GTATGCTCTC
*
15883314 ACAAGCTGTAAATTGGTAAGCTCAT
1 ACAAGCTGAAAATTGGTAAGCTCAT
* * *
15883339 ACGAGCTGAGAATTGGTAAGATC-T
1 ACAAGCTGAAAATTGGTAAGCTCAT
15883363 CACAAGCT-AAAATTGGTAAGCTCAT
1 -ACAAGCTGAAAATTGGTAAGCTCAT
15883388 ACAAGCT
1 ACAAGCT
15883395 AAGAATCGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 21 0.45
25 26 0.55
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (25 bp):
ACAAGCTGAAAATTGGTAAGCTCAT
Found at i:15884869 original size:54 final size:54
Alignment explanation
Indices: 15884811--15884924 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
15884801 TTAGTTGTTC
* * *
15884811 GAATAAATTACTCATATTATTTAATTGAGTT-TATCTTAGTTAATTAAGTTGCTG
1 GAATAAATTACTCATATTAGTTAATTAAGTTCT-TCTTAGTCAATTAAGTTGCTG
* *
15884865 GAATAAATTACTCATCTTAGTTAATTAAGTTCTTCTTAGTCAATTTAGTTGCTG
1 GAATAAATTACTCATATTAGTTAATTAAGTTCTTCTTAGTCAATTAAGTTGCTG
15884919 GAATAA
1 GAATAA
15884925 TTTATTGTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (54 bp):
GAATAAATTACTCATATTAGTTAATTAAGTTCTTCTTAGTCAATTAAGTTGCTG
Found at i:15885203 original size:24 final size:23
Alignment explanation
Indices: 15885168--15885249 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
15885158 AAAGGGTTGT
*
15885168 TACATCAATTAAAGGAGAGAATTA
1 TACATCATTTAAAGGAGAG-ATTA
*
15885192 TACATCATTTAAAGGAGTCG-TTA
1 TACATCATTTAAAGGAG-AGATTA
*
15885215 T--ATCATTTAAAGGAAAGCATTA
1 TACATCATTTAAAGGAGAG-ATTA
*
15885237 TACATCCTTTAAA
1 TACATCATTTAAA
15885250 ATTCGGTAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 4 0.08
23 4 0.08
24 25 0.52
25 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (23 bp):
TACATCATTTAAAGGAGAGATTA
Found at i:15885225 original size:45 final size:44
Alignment explanation
Indices: 15885158--15885249 Score: 121
Period size: 45 Copynumber: 2.1 Consensus size: 44
15885148 GGTTACATAC
* *
15885158 AAAGGGTTGTTACATCAATTAAAGGAGAGAATTATACATCATTT
1 AAAGGGTCGTTACATCAATTAAAGGAAAGAATTATACATCATTT
* * * *
15885202 AAAGGAGTCGTTATATCATTTAAAGGAAAGCATTATACATCCTTT
1 AAAGG-GTCGTTACATCAATTAAAGGAAAGAATTATACATCATTT
15885247 AAA
1 AAA
15885250 ATTCGGTAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 5 0.12
45 36 0.88
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (44 bp):
AAAGGGTCGTTACATCAATTAAAGGAAAGAATTATACATCATTT
Found at i:15887699 original size:13 final size:13
Alignment explanation
Indices: 15887678--15887712 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
15887668 ATAAGTTGTT
* *
15887678 GTTAGTTAAATTA
1 GTTAATTAAATAA
15887691 GTTAATTAAATAA
1 GTTAATTAAATAA
15887704 GTTAATTAA
1 GTTAATTAA
15887713 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:15888645 original size:13 final size:13
Alignment explanation
Indices: 15888627--15888651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15888617 AACAACTAGG
15888627 AGCTTTAATTTCC
1 AGCTTTAATTTCC
15888640 AGCTTTAATTTC
1 AGCTTTAATTTC
15888652 ATTCAGCCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (13 bp):
AGCTTTAATTTCC
Found at i:15888703 original size:14 final size:14
Alignment explanation
Indices: 15888684--15888725 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
15888674 TAGTTTAATG
15888684 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
15888698 ATTTTTATTTATTT
1 ATTTTTATTTTTTT
15888712 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
15888726 AAGTTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:15892499 original size:13 final size:13
Alignment explanation
Indices: 15892478--15892512 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
15892468 ATAAGTTGCT
* *
15892478 GTTAGTTAAATTA
1 GTTAATTAAATAA
15892491 GTTAATTAAATAA
1 GTTAATTAAATAA
15892504 GTTAATTAA
1 GTTAATTAA
15892513 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:15893488 original size:14 final size:14
Alignment explanation
Indices: 15893469--15893510 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
15893459 TAGTTTAATG
15893469 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
15893483 ATTTTTATTTATTT
1 ATTTTTATTTTTTT
15893497 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
15893511 AAGTTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:15895598 original size:19 final size:19
Alignment explanation
Indices: 15895574--15895612 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15895564 AATAAATTAC
*
15895574 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
15895593 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
15895612 T
1 T
15895613 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:15900553 original size:21 final size:22
Alignment explanation
Indices: 15900518--15900558 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
15900508 TAGGTGTTAA
15900518 ATAAAAAAATCATTAAAAATTC
1 ATAAAAAAATCATTAAAAATTC
*
15900540 ATAAAAATAT-ATTAAAAAT
1 ATAAAAAAATCATTAAAAAT
15900559 CCAGTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAAAAAATCATTAAAAATTC
Found at i:15906603 original size:23 final size:23
Alignment explanation
Indices: 15906573--15906616 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15906563 ATTTAAGGCC
15906573 GATTCCTTGCTACCAACAAGACT
1 GATTCCTTGCTACCAACAAGACT
*
15906596 GATTCCTTGCTGCCAACAAGA
1 GATTCCTTGCTACCAACAAGA
15906617 GAAAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.25
Consensus pattern (23 bp):
GATTCCTTGCTACCAACAAGACT
Found at i:15906915 original size:25 final size:25
Alignment explanation
Indices: 15906887--15906934 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
15906877 CAACTTCTAA
*
15906887 AGAAAA-CTCAAGAGAGAATTCTTGG
1 AGAAAACCTCAA-AGAAAATTCTTGG
15906912 AGAAAACCTCAAAGAAAATTCTT
1 AGAAAACCTCAAAGAAAATTCTT
15906935 CTCTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (25 bp):
AGAAAACCTCAAAGAAAATTCTTGG
Found at i:15910875 original size:21 final size:19
Alignment explanation
Indices: 15910832--15910876 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
15910822 GAGCTCAAAT
* *
15910832 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
15910851 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
15910872 GAGCT
1 GAGCT
15910877 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:15912361 original size:23 final size:23
Alignment explanation
Indices: 15912331--15912376 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
15912321 GGATTTAAGG
15912331 CCGATTCCTTGCTACCAACAAGA
1 CCGATTCCTTGCTACCAACAAGA
*
15912354 CCGATTCCTTGCTGCCAACAAGA
1 CCGATTCCTTGCTACCAACAAGA
15912377 GAAAGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.22
Consensus pattern (23 bp):
CCGATTCCTTGCTACCAACAAGA
Found at i:15912675 original size:25 final size:25
Alignment explanation
Indices: 15912647--15912694 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
15912637 CAACTTCTAA
*
15912647 AGAAAA-CTCAAGAGAGAATTCTTGG
1 AGAAAACCTCAA-AGAAAATTCTTGG
15912672 AGAAAACCTCAAAGAAAATTCTT
1 AGAAAACCTCAAAGAAAATTCTT
15912695 CTCTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (25 bp):
AGAAAACCTCAAAGAAAATTCTTGG
Found at i:15914192 original size:18 final size:18
Alignment explanation
Indices: 15914166--15914213 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
15914156 TAGTAGTATA
15914166 AAATATAAAAGTAAAAACC
1 AAAT-TAAAAGTAAAAACC
* * *
15914185 CAATTAAAAATTTAAAACC
1 AAATT-AAAAGTAAAAACC
15914204 AAATTAAAAG
1 AAATTAAAAG
15914214 GCCTTATTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (18 bp):
AAATTAAAAGTAAAAACC
Found at i:15914490 original size:8 final size:8
Alignment explanation
Indices: 15914477--15914508 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
15914467 ATAAACCTTG
15914477 AACCCTAA
1 AACCCTAA
15914485 AACCCT-A
1 AACCCTAA
15914492 AACCCTAA
1 AACCCTAA
15914500 AACCCTAA
1 AACCCTAA
15914508 A
1 A
15914509 CCTTAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (8 bp):
AACCCTAA
Found at i:15914494 original size:7 final size:7
Alignment explanation
Indices: 15914477--15914527 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
15914467 ATAAACCTTG
15914477 AACCCTAA
1 AACCCT-A
15914485 AACCCTA
1 AACCCTA
15914492 AACCCTAA
1 AACCCT-A
15914500 AACCCTA
1 AACCCTA
*
15914507 AACCTTA
1 AACCCTA
*
15914514 AACCCTT
1 AACCCTA
15914521 AACCCTA
1 AACCCTA
15914528 TATCAGAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 25 0.66
8 13 0.34
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:15914495 original size:15 final size:15
Alignment explanation
Indices: 15914477--15914527 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
15914467 ATAAACCTTG
15914477 AACCCTAAAACCCTA
1 AACCCTAAAACCCTA
15914492 AACCCTAAAACCCTA
1 AACCCTAAAACCCTA
* *
15914507 AA-CCTTAAACCCTT
1 AACCCTAAAACCCTA
15914521 AACCCTA
1 AACCCTA
15914528 TATCAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCCTAAAACCCTA
Found at i:15914520 original size:8 final size:8
Alignment explanation
Indices: 15914468--15914526 Score: 56
Period size: 7 Copynumber: 8.0 Consensus size: 8
15914458 GTGTGGGCCA
15914468 TAAA-CCT
1 TAAACCCT
*
15914475 TGAACCCT
1 TAAACCCT
*
15914483 AAAACCC-
1 TAAACCCT
15914490 TAAACCCT
1 TAAACCCT
*
15914498 AAAACCC-
1 TAAACCCT
15914505 TAAA-CCT
1 TAAACCCT
15914512 TAAACCCT
1 TAAACCCT
15914520 T-AACCCT
1 TAAACCCT
15914527 ATATCAGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 2 0.05
7 22 0.52
8 18 0.43
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (8 bp):
TAAACCCT
Found at i:15914896 original size:107 final size:107
Alignment explanation
Indices: 15914672--15914977 Score: 356
Period size: 107 Copynumber: 2.9 Consensus size: 107
15914662 AGGGGTATAA
* * * *
15914672 CAGTCATTTTACCCTT-TAGGGGTATTTCGGTAATTTTACTCTTTGAAGGTATTTTAGTAATTTT
1 CAGT-ATTTTACCCTTCGA-GGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAGTAATTTT
* *
15914736 A-CCATTCAGGAGTATTTCGATAATTTTACCCTTTAGGGATATTT
64 ACCCATTGAGG-GTATTTCGATAATTTTACCCTTAAGGGATATTT
* *
15914780 CAGTGTTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTTGAGGGTATTTC-GATAA-TTTA
1 CAGTATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAG-TAATTTTA
*
15914843 CCCATTGAGGGTATTTC-AGTTATTTTACCCTTCAAGGG-TATTT
65 CCCATTGAGGGTATTTCGA-TAATTTTACCCTT-AAGGGATATTT
* * **
15914886 CGGTAATTTTACCCTTCGAGGGTATTTTGGTAATTTTACCCTTCAAGGGTATTTCAGTAATTTTA
1 CAGT-ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAGTAATTTTA
* *
15914951 CCC-TTCGAGGGCATTTCGATAGTTTTA
65 CCCATT-GAGGGTATTTCGATAATTTTA
15914978 TCCACAAATC
Statistics
Matches: 170, Mismatches: 18, Indels: 20
0.82 0.09 0.10
Matches are distributed among these distances:
105 1 0.01
106 32 0.19
107 107 0.63
108 29 0.17
109 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (107 bp):
CAGTATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAGTAATTTTAC
CCATTGAGGGTATTTCGATAATTTTACCCTTAAGGGATATTT
Found at i:15914956 original size:27 final size:27
Alignment explanation
Indices: 15914672--15914967 Score: 320
Period size: 27 Copynumber: 11.0 Consensus size: 27
15914662 AGGGGTATAA
* *
15914672 CAGTCATTTTACCCTT-TAGGGGTATTT
1 CAGTAATTTTACCCTTCGA-GGGTATTT
* * * *
15914699 CGGTAATTTTACTCTTTGAAGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
15914726 TAGTAATTTTACCATTC-AGGAGTATTT
1 CAGTAATTTTACCCTTCGAGG-GTATTT
*
15914753 C-GATAATTTTACCCTT-TAGGGATATTT
1 CAG-TAATTTTACCCTTCGAGGG-TATTT
*
15914780 CAGT-GTTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
15914806 CAGTAATTTTACCCTTTGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
15914833 C-GATAA-TTTACCCATT-GAGGGTATTT
1 CAG-TAATTTTACCC-TTCGAGGGTATTT
* *
15914859 CAGTTATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
15914886 CGGTAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
** *
15914913 TGGTAATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
15914940 CAGTAATTTTACCCTTCGAGGGCATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
15914967 C
1 C
15914968 GATAGTTTTA
Statistics
Matches: 228, Mismatches: 28, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
26 46 0.20
27 180 0.79
28 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGAGGGTATTT
Found at i:15923755 original size:495 final size:495
Alignment explanation
Indices: 15922820--15923790 Score: 1627
Period size: 495 Copynumber: 2.0 Consensus size: 495
15922810 TCAATACAAC
* *
15922820 TCACAAAGGCCCAACCCAAGCTCAAGAACGTGATGGGCTCAAATTACTACAAGGCCCAATAACGA
1 TCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACGA
* * * *
15922885 GGTCAAAGGCCAGACAAAGGTGTTCCAAACTAAATGGGACCATTCAGGAATTTGTTAGCAAGGCC
66 GATCAAAGGCCAGACAAAGGCGTTCCAAACTAAATGGGACCATCCAGGAATTCGTTAGCAAGGCC
* *
15922950 TTAGATGCGTACACGAAATAAAGAGAAAATCAAGATTCACTTTCTTATTTTCAAGAAAATCAAGA
131 TTAGATGCATACACGAAAGAAAGAGAAAATCAAGATTCACTTTCTTATTTTCAAGAAAATCAAGA
* * *
15923015 AACCGAATCTTGGCCCAATTTTGCTGTTTGGAGTGATTTCAAGAATCAAGAAAATCAAGATTTCA
196 AACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAAAAAATCAAGATTTCA
*
15923080 AATCTTGGAAATCTTGGTCCAAGAAACCGAATCTTGCAGCCAAAGCACATTGGATCTCCGTTACA
261 AATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCAGCCAAAGCACATTGGATCTCCGTTACA
* *
15923145 AGCATCAACGAACCAATTTCGGTAGGAGATGGACTACAAGCCCAAGTTCTTGAAGGCAAGGCCCA
326 AGCATCAACGAACCAATTTCGGTAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGCCCA
* * * * * *
15923210 ATAAGATGATTCCAAGCCCAACCAAGAAGTCAAACCATACTTAGTTGAAAATTAGGCCAAATTGT
391 ATAAGATAAGTCCAAGCCCAAACAAGAAGACAAACCATACTTACTTGAAAATCAGGCCAAATTGT
* *
15923275 TAAAGTGGCCCAATTTGTAAAAGATTTTAATTGATACGAG
456 CAAAATGGCCCAATTTGTAAAAGATTTTAATTGATACGAG
*
15923315 TCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAATGA
1 TCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACGA
* * *
15923380 GATCAAAGGCCCGACAAATGCGTTCCAAACTAAATGGGACCATCCAGGAGTTCGTTAGCAAGGCC
66 GATCAAAGGCCAGACAAAGGCGTTCCAAACTAAATGGGACCATCCAGGAATTCGTTAGCAAGGCC
* * *
15923445 TTAGATGCATATACGAGAGAAAGAGAAAATCAAGATTCACTTTCTTATTTTCAAGAAGATCAAGA
131 TTAGATGCATACACGAAAGAAAGAGAAAATCAAGATTCACTTTCTTATTTTCAAGAAAATCAAGA
*
15923510 AACCGAATCTTGGCCTAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAAAAAATCAAGATTTCA
196 AACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAAAAAATCAAGATTTCA
* *
15923575 AATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCAGCCAAATCACATTGGATCTCCGTTACG
261 AATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCAGCCAAAGCACATTGGATCTCCGTTACA
* *
15923640 AGCCTCAACGACCCAATTTCGGTAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGCCCA
326 AGCATCAACGAACCAATTTCGGTAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGCCCA
*
15923705 ATAAGATAAGTCCAAGCCCAAACAAGAAGACAAACCATACTTACTTGAAAATCAGGCCCAATTGT
391 ATAAGATAAGTCCAAGCCCAAACAAGAAGACAAACCATACTTACTTGAAAATCAGGCCAAATTGT
15923770 CAAAATGGCCCAATTTGTAAA
456 CAAAATGGCCCAATTTGTAAA
15923791 GTTTTATTTT
Statistics
Matches: 441, Mismatches: 35, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
495 441 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (495 bp):
TCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGCCCAATAACGA
GATCAAAGGCCAGACAAAGGCGTTCCAAACTAAATGGGACCATCCAGGAATTCGTTAGCAAGGCC
TTAGATGCATACACGAAAGAAAGAGAAAATCAAGATTCACTTTCTTATTTTCAAGAAAATCAAGA
AACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAAAAAATCAAGATTTCA
AATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCAGCCAAAGCACATTGGATCTCCGTTACA
AGCATCAACGAACCAATTTCGGTAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGCCCA
ATAAGATAAGTCCAAGCCCAAACAAGAAGACAAACCATACTTACTTGAAAATCAGGCCAAATTGT
CAAAATGGCCCAATTTGTAAAAGATTTTAATTGATACGAG
Found at i:15933055 original size:20 final size:19
Alignment explanation
Indices: 15933007--15933055 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
15932997 ATTCAACTCA
15933007 ATTTTAGCTCAATGAGCTC
1 ATTTTAGCTCAATGAGCTC
*
15933026 GTTCTTAGCTCAATGAGCTC
1 ATT-TTAGCTCAATGAGCTC
15933046 ATTTTCAGCT
1 ATTTT-AGCT
15933056 TACTTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (19 bp):
ATTTTAGCTCAATGAGCTC
Found at i:15938701 original size:21 final size:22
Alignment explanation
Indices: 15938672--15938722 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
15938662 TCTCTCTCGC
*
15938672 TTTCCTTTTCTCCTTTTTCA-T
1 TTTCATTTTCTCCTTTTTCACT
*
15938693 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCTCCTTTTTCACT
15938715 TTT-ATTTT
1 TTTCATTTT
15938723 TCTCTTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCATTTTCTCCTTTTTCACT
Found at i:15938728 original size:21 final size:20
Alignment explanation
Indices: 15938672--15938728 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
15938662 TCTCTCTCGC
*
15938672 TTTCCTTTTCTCCTTTTTCAT
1 TTTCATTTTCT-CTTTTTCAT
15938693 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTC-TCTTTTTCA-T
15938715 TTT-ATTTTTCTCTT
1 TTTCA-TTTTCTCTT
15938729 CTCCTTTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTCATTTTCTCTTTTTCAT
Found at i:15940887 original size:24 final size:24
Alignment explanation
Indices: 15940840--15940887 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
15940830 TGAGCGCAAA
15940840 TTCTCTTGAGTTTTTTTCCAAGAATT
1 TTCTCTTGAGTTTTTTT-C-AGAATT
15940866 TTCTCTTGAGTTTTCTTT-AGAA
1 TTCTCTTGAGTTTT-TTTCAGAA
15940888 GTAGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
26 14 0.67
27 3 0.14
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (24 bp):
TTCTCTTGAGTTTTTTTCAGAATT
Found at i:15942558 original size:9 final size:9
Alignment explanation
Indices: 15942544--15942569 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
15942534 GGTCAAGGTG
15942544 ATAATGATC
1 ATAATGATC
15942553 ATAATGATC
1 ATAATGATC
15942562 ATAATGAT
1 ATAATGAT
15942570 GTCTACCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (9 bp):
ATAATGATC
Found at i:15946033 original size:29 final size:27
Alignment explanation
Indices: 15945995--15946049 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
15945985 GTGATTAAAT
15945995 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
15946024 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
15946050 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:15947215 original size:42 final size:42
Alignment explanation
Indices: 15947156--15947238 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
15947146 AAATTCAAAG
* *
15947156 GGATAAGAACAAGAGTTCAAATGTTTGACTTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATATTTGAATTTCAAACGTTTT
15947198 GGATAAGAACAAGAGTTCAAATATTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATATTTGAATTTCAAACGTTT
15947239 CACACATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATATTTGAATTTCAAACGTTTT
Found at i:15968576 original size:29 final size:29
Alignment explanation
Indices: 15968532--15968589 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
15968522 CGTTCTTGGG
15968532 CTTGGGTTGGGCCTTTGTGACTCGTATCA
1 CTTGGGTTGGGCCTTTGTGACTCGTATCA
*
15968561 CTTGGGTTGGGTCTTTGTGACTCGTATCA
1 CTTGGGTTGGGCCTTTGTGACTCGTATCA
15968590 TTCCCCCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.10, C:0.19, G:0.31, T:0.40
Consensus pattern (29 bp):
CTTGGGTTGGGCCTTTGTGACTCGTATCA
Found at i:15980867 original size:12 final size:12
Alignment explanation
Indices: 15980852--15980882 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
15980842 CTTTTCTTTT
15980852 TTTTTTTCACAA
1 TTTTTTTCACAA
*
15980864 TTTTTTTCACGA
1 TTTTTTTCACAA
15980876 TTTTTTT
1 TTTTTTT
15980883 TGCTTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:15985066 original size:21 final size:22
Alignment explanation
Indices: 15985037--15985087 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
15985027 TTTCTCTCGC
*
15985037 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
15985058 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
15985080 TTT-ATTTT
1 TTTCATTTT
15985088 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:15985634 original size:21 final size:22
Alignment explanation
Indices: 15985601--15985655 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
15985591 TGTTTCTCTC
*
15985601 TCAC-TTTCCTTTTCGCCTTTT
1 TCACTTTTCATTTTCGCCTTTT
**
15985622 TCA-TTTTCATTTTCTTCTTTT
1 TCACTTTTCATTTTCGCCTTTT
15985643 TCACTTTT-ATTTT
1 TCACTTTTCATTTT
15985656 TCTCTTCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (22 bp):
TCACTTTTCATTTTCGCCTTTT
Found at i:15985819 original size:569 final size:568
Alignment explanation
Indices: 15984694--15986129 Score: 2642
Period size: 569 Copynumber: 2.5 Consensus size: 568
15984684 TTCAAAATTC
*
15984694 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATAAAGTTGTTTAGAGAATAGAGAAACTTCACC
1 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTGTTTAGAGAATAGAGAAACTTCACC
* * *
15984759 TTGCTTACCATTAGAGGTGGGAAAACGAGGACCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
66 TTGCTTACCGTTAGAGGTGGGAAAATGAGGATCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
15984824 TCTC-AGTAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAA
131 TCTCGA-TAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAA
* *
15984888 AGAGAAATCACAAGGCGATTTCAAATGGGGGTTAGCAAAAATATTCCTCCATTGTGTTTGAGCAC
195 AGAGAAATCACAAGGCGATTTCGAATGGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCAC
*
15984953 TCTCTTTTTCTTCACTCATTCCTTATTTAAGCTCTCTCTCTTTTTCACTCACTTCATTCACATTT
260 TCTCTTTTTCTTCACTCATTCCTTGTTTAAGCTCT-TCTCTTTTTCACTCACTTCATTCACATTT
* *
15985018 TCTTTTGTTTTTCTCTCGCTTTCCTTTTCGCCTTTTTCATTTTCATTTTCTTCTTTTTCACTTTT
324 TCTTTTGTTTCTCTCTCACTTTCCTTTTCGCCTTTTTCATTTTCATTTTCTTCTTTTTCACTTTT
*
15985083 ATTTTTCTCTTCTCCTTTTTCTTTTTCCTCACTTGTTTTAACAACAGAATTTTTCAGTTTGATTT
389 ATTTTTCTCTTCTCCTTTCTCTTTTTCCTCACTTGTTTTAACAACAGAATTTTTCAGTTTGATTT
*
15985148 GGTCCTCATGGACATGTTCCGGAGTGAGTGGCACTAAGGTGACTTTCCTTCCTTGATGCTTGAAA
454 GGTCCTCATGGACATGTTCCGGAGTGAGCGGCACTAAGGTGACTTTCCTTCCTTGATGCTTGAAA
15985213 GAATACCCATTGGTACGACCATCGTGGGTGACTTTCGATCCCTTTGCCAT
519 GAATACCCATTGGTACGACCATCGTGGGTGACTTTCGATCCCTTTGCCAT
**
15985263 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTGTTTAGAGAATAGAGAAACTTCATA
1 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTGTTTAGAGAATAGAGAAACTTCACC
*
15985328 TTGCTTACCGTTAGAGGTGGGAAAATGAGGGTCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
66 TTGCTTACCGTTAGAGGTGGGAAAATGAGGATCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
15985393 TCTCGATAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAAA
131 TCTCGATAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAAA
15985458 GAGAAATCACAAGGCGATTTCGAATGGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCACT
196 GAGAAATCACAAGGCGATTTCGAATGGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCACT
15985523 CTCTTTTTCTTCACTCATTCCTTGTTTAAGCTCTTCTCTTTTTCACTCACTTCATTCACATTTTC
261 CTCTTTTTCTTCACTCATTCCTTGTTTAAGCTCTTCTCTTTTTCACTCACTTCATTCACATTTTC
15985588 TTTTGTTTCTCTCTCACTTTCCTTTTCGCCTTTTTCATTTTCATTTTCTTCTTTTTCACTTTTAT
326 TTTTGTTTCTCTCTCACTTTCCTTTTCGCCTTTTTCATTTTCATTTTCTTCTTTTTCACTTTTAT
15985653 TTTTCTCTTCTCCTTTCTCTTTTTCCTCACTTGTTTTAACAACAGAATTTTTCAGTTTGATTTGG
391 TTTTCTCTTCTCCTTTCTCTTTTTCCTCACTTGTTTTAACAACAGAATTTTTCAGTTTGATTTGG
*
15985718 TCCTCATGGACATGTTTCGGAGTGAGCGGCACTAAGGTGACTTTCCTTCCTTGATGCTTGAAAGA
456 TCCTCATGGACATGTTCCGGAGTGAGCGGCACTAAGGTGACTTTCCTTCCTTGATGCTTGAAAGA
15985783 ATACCCATTGGTACGACCATCGTGGGTGACCTTTCGATCCCTTTGCCAT
521 ATACCCATTGGTACGACCATCGTGGGTGA-CTTTCGATCCCTTTGCCAT
*
15985832 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTATTTAGAGAATAGAGAAACTTCACC
1 AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTGTTTAGAGAATAGAGAAACTTCACC
*
15985897 TTGCTTACCGTTAGAGGTGGGAAAATGAGGATCAGTTTTACCTTGTTCAATCAATTGAAAATGTC
66 TTGCTTACCGTTAGAGGTGGGAAAATGAGGATCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
* *
15985962 TCTCGGTAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAAACTTGCAAACCTGAAACAAA
131 TCTCGATAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAAA
*
15986027 GAGAAATCACAAGGCGATTTCGAATAGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCACT
196 GAGAAATCACAAGGCGATTTCGAATGGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCACT
*
15986092 CTCTTCTTCTTCACTCATTCCTTGTTTAAGCTC-TCTCT
261 CTCTTTTTCTTCACTCATTCCTTGTTTAAGCTCTTCTCT
15986130 GATGTGCGCA
Statistics
Matches: 841, Mismatches: 24, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
568 255 0.30
569 585 0.70
570 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (568 bp):
AAGTCATGAGCAAAGTCATCAATACGAGTTGAATGAAGTTGTTTAGAGAATAGAGAAACTTCACC
TTGCTTACCGTTAGAGGTGGGAAAATGAGGATCAGTTTTACCTTGTTCAATCAATTGAAAACGTC
TCTCGATAGAAGGGTAATGAAGTTGGAACCTGTCCATGGGTGGAATCTTGCAAACCTGAAACAAA
GAGAAATCACAAGGCGATTTCGAATGGGGGTTAGCAAAAATATTCCTCCCTTGTGTTTGAGCACT
CTCTTTTTCTTCACTCATTCCTTGTTTAAGCTCTTCTCTTTTTCACTCACTTCATTCACATTTTC
TTTTGTTTCTCTCTCACTTTCCTTTTCGCCTTTTTCATTTTCATTTTCTTCTTTTTCACTTTTAT
TTTTCTCTTCTCCTTTCTCTTTTTCCTCACTTGTTTTAACAACAGAATTTTTCAGTTTGATTTGG
TCCTCATGGACATGTTCCGGAGTGAGCGGCACTAAGGTGACTTTCCTTCCTTGATGCTTGAAAGA
ATACCCATTGGTACGACCATCGTGGGTGACTTTCGATCCCTTTGCCAT
Found at i:16046592 original size:14 final size:14
Alignment explanation
Indices: 16046570--16046608 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
16046560 AGACCGCATG
*
16046570 CAATATTTTTTTTT
1 CAATTTTTTTTTTT
*
16046584 CAATTTTTTTCTTT
1 CAATTTTTTTTTTT
*
16046598 CGATTTTTTTT
1 CAATTTTTTTT
16046609 GATTTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (14 bp):
CAATTTTTTTTTTT
Found at i:16075528 original size:19 final size:19
Alignment explanation
Indices: 16075500--16075554 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
16075490 GCGAAAATAC
*
16075500 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
16075520 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
16075539 AAAAGAGAATGAAAAA
1 AAAAGA-AA-GAAAAA
16075555 AAAATGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.60
20 7 0.23
21 5 0.17
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:16075571 original size:14 final size:14
Alignment explanation
Indices: 16075547--16075588 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
16075537 AAAAAAGAGA
16075547 ATGAAAA-AAAAATG
1 ATGAAAAGAAAAA-G
16075561 A-GAAAAGAAAAAG
1 ATGAAAAGAAAAAG
16075574 ATGAAAAAGAAAAAG
1 ATG-AAAAGAAAAAG
16075589 TGATTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 7 0.28
15 11 0.44
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (14 bp):
ATGAAAAGAAAAAG
Found at i:16075571 original size:15 final size:15
Alignment explanation
Indices: 16075552--16075588 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
16075542 AGAGAATGAA
*
16075552 AAAAAAATGAGAAAAG
1 AAAAAGATGA-AAAAG
16075568 AAAAAGATGAAAAAG
1 AAAAAGATGAAAAAG
16075583 AAAAAG
1 AAAAAG
16075589 TGATTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAAGATGAAAAAG
Found at i:16079834 original size:23 final size:23
Alignment explanation
Indices: 16079802--16079913 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
16079792 CTTTTTGAAC
* *
16079802 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
16079825 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
16079848 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
16079871 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
16079894 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
16079914 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:16079878 original size:46 final size:46
Alignment explanation
Indices: 16079802--16079913 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
16079792 CTTTTTGAAC
* *
16079802 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
16079848 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
16079894 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
16079914 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:16106327 original size:20 final size:19
Alignment explanation
Indices: 16106297--16106346 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
16106287 TCACTCTCAA
16106297 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCT-TTTTTCAT
*
16106318 TCTCTTTTTCTTTTTTGAT
1 TCTCTTTTTCTTTTTTCAT
16106337 T-TCTTTTTCT
1 TCTCTTTTTCT
16106347 GTCTTCCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 7 0.25
21 4 0.14
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (19 bp):
TCTCTTTTTCTTTTTTCAT
Found at i:16106331 original size:18 final size:17
Alignment explanation
Indices: 16106303--16106346 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
16106293 TCAATCTCTT
16106303 TTTTCTCTTTTTCATTCTC
1 TTTT-TCTTTTTCATT-TC
*
16106322 TTTTTCTTTTTTGATTTC
1 TTTTTC-TTTTTCATTTC
16106340 TTTTTCT
1 TTTTTCT
16106347 GTCTTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTTTCATTTC
Found at i:16108193 original size:21 final size:22
Alignment explanation
Indices: 16108168--16108208 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16108158 GTAGTTAATG
16108168 TTGTGT-TTACTGCTGAATTAA
1 TTGTGTCTTACTGCTGAATTAA
**
16108189 TTGTGTCTTGTTGCTGAATT
1 TTGTGTCTTACTGCTGAATT
16108209 CTAGTCCAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.10, G:0.22, T:0.51
Consensus pattern (22 bp):
TTGTGTCTTACTGCTGAATTAA
Found at i:16110995 original size:514 final size:516
Alignment explanation
Indices: 16109776--16111316 Score: 2362
Period size: 514 Copynumber: 3.0 Consensus size: 516
16109766 TATTAGTTTC
* * * *
16109776 CTAACCCTATTAGGAAAAACT-AAAAAAACCCTAATTATTTGA---TTAAAGGAAAATTCGGCCA
1 CTAACCCTATTAGG-AAAACTAAAAAAAACCCTAATTA-TTGACTTTTCAAGGGATATTCGACCA
* * * * * * * *
16109837 AGGCTATTTAAATGGGCCTCTTGGACTGAATGTTTACATAGAAATTAATTTATGAAGTCTAA-AA
64 AGGC-CTTT-AATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTCTAACAA
* * * *
16109901 TTTAAACTAAGTATTTAAAGAATTAAAACTTAACAAATTGGGCCACTTTGACAATTTGGCCTGAT
127 TTAAAACTAAATATTTAAAGAATTAAAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGAT
16109966 TTTTAACTAAATTTGATTTAAATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTA
192 TTTTAACTAAATTTGATTTAAATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTA
16110031 AGAACTTGGGCTTGTAATCCGTTCTCTCCCGAAATTGGCTTGTTAATGCTCGTAACTGAGATCCA
257 AGAACTTGGGCTTGTAATCCGTTCTCTCCCGAAATTGGCTTGTTAATGCTCGTAACTGAGATCCA
*
16110096 ATGTGCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTT
322 ATGCGCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTT
* * *
16110161 CTTGATTCTTAAAATCGATCAAAACAGCAAAATTAGACCAAGATTCGGTTTCTTGATTTTCTTGA
387 CTTGATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGA-----TTTCTTGATTTTCTTGA
* *
16110226 AAATAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACTCATCTAAGGCCTTTGTGACTCA
447 AAACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCA
16110291 TATCA
512 TATCA
16110296 CTAACCCTATTAGGAAAACTAAAAAAAACCCTAATTATTGACTTTTCAAGGGATATTCGACCAAG
1 CTAACCCTATTAGGAAAACTAAAAAAAACCCTAATTATTGACTTTTCAAGGGATATTCGACCAAG
16110361 GCCTTTAATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTCTAACAATTAA
66 GCCTTTAATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTCTAACAATTAA
16110426 AACTAAATATTTAAAGAATTAAAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTT
131 AACTAAATATTTAAAGAATTAAAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTT
*
16110491 AACTAAATTTGATTTATATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTAAGAA
196 AACTAAATTTGATTTAAATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTAAGAA
*
16110556 CTTGGGCTTGTAATCCGTTCTCTCCCAAAATTGGCTTGTTAATGCTCGTAACTGAGATCCAATGC
261 CTTGGGCTTGTAATCCGTTCTCTCCCGAAATTGGCTTGTTAATGCTCGTAACTGAGATCCAATGC
16110621 GCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTG
326 GCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTG
*
16110686 ATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGA-TT-TGGATTTTCTTGAAAACAAGAA
391 ATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGATTTCTTGATTTTCTTGAAAACAAGAA
*
16110749 AGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCGTATCA
456 AGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCATATCA
*
16110810 CTAACCCTATAAGGAAAACTAAAAAAAACCCTAATTATTGACTTTTCAAGGGATATTCGACCAAG
1 CTAACCCTATTAGGAAAACTAAAAAAAACCCTAATTATTGACTTTTCAAGGGATATTCGACCAAG
*
16110875 GCCTTTAATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTTTAACAATTAA
66 GCCTTTAATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTCTAACAATTAA
*
16110940 AACTAAATATTTAAAGAATTAGAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTT
131 AACTAAATATTTAAAGAATTAAAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTT
* * * * * * * * * * *
16111005 CAACTAAGTCTAATTTAAACTTCTTGGTTGGGCCTGGAACATCTTATTGGGCCGTATC-TCAAGA
196 -AACTAAATTTGATTTAAATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTAAGA
* * * *
16111069 ACTTGGGCTTGTAATCCGTTCTCTCTCGAAATTGG-TTCATTGATGCTCGTAACTGAGATCTAAT
260 ACTTGGGCTTGTAATCCGTTCTCTCCCGAAATTGGCTT-GTTAATGCTCGTAACTGAGATCCAAT
* * * * * * *
16111133 GCGCTTTAGCTGCAGGATTCAGTTTATTGGGCCAGGATTTCCAAGATTTGAAATCTTGATTTTCT
324 GCGCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCT
* * *
16111198 TGATTCTTGAAATCGCTCAAAATAACAAAATTGGGCCAAGATTCGGTTTCTTGATTTTCTTGAAA
389 TGATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGA-----TTTCTTGATTTTCTTGAAA
* * *
16111263 ACAAGAAAATGAATCTTGATTTTCTTTTTCCTTTGTATATGCATCTAAGGCCTT
449 ACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTT
16111317 GCTAATGAAG
Statistics
Matches: 947, Mismatches: 60, Indels: 27
0.92 0.06 0.03
Matches are distributed among these distances:
513 2 0.00
514 428 0.45
515 48 0.05
519 10 0.01
520 77 0.08
521 363 0.38
522 19 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (516 bp):
CTAACCCTATTAGGAAAACTAAAAAAAACCCTAATTATTGACTTTTCAAGGGATATTCGACCAAG
GCCTTTAATGGGCTTCTTGGGCTGAATTTTTATATAGGAATTTATTTATAAAGTCTAACAATTAA
AACTAAATATTTAAAGAATTAAAATTTCACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTT
AACTAAATTTGATTTAAATTTCTAGATTGGGCTTCGAACATCTTATTGGGCCTTGTCTTTAAGAA
CTTGGGCTTGTAATCCGTTCTCTCCCGAAATTGGCTTGTTAATGCTCGTAACTGAGATCCAATGC
GCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTG
ATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGATTTCTTGATTTTCTTGAAAACAAGAA
AGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCATATCA
Found at i:16116565 original size:46 final size:46
Alignment explanation
Indices: 16116515--16116605 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
16116505 TGGTAATTTG
16116515 AGCCCATCACGTTCTTAGGCTTGGGTTGGGCCTTTGTGACTCGTAC
1 AGCCCATCACGTTCTTAGGCTTGGGTTGGGCCTTTGTGACTCGTAC
*
16116561 AGCCCATCACGTTCTTGGGCTTGGGTTGGGCCTTTGTGACTCGTA
1 AGCCCATCACGTTCTTAGGCTTGGGTTGGGCCTTTGTGACTCGTA
16116606 TCATTCCCCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.12, C:0.25, G:0.30, T:0.33
Consensus pattern (46 bp):
AGCCCATCACGTTCTTAGGCTTGGGTTGGGCCTTTGTGACTCGTAC
Found at i:16122760 original size:48 final size:48
Alignment explanation
Indices: 16122689--16122784 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
16122679 CCTTTAAATA
16122689 CTTCAAGGACTCATGATCGGTGTGTATGACGAATTCCTTGGGCCAAAG
1 CTTCAAGGACTCATGATCGGTGTGTATGACGAATTCCTTGGGCCAAAG
16122737 CTTCAAGGACTCATGATCGGTGTGTATGACGAATTCCTTGGGCCAAAG
1 CTTCAAGGACTCATGATCGGTGTGTATGACGAATTCCTTGGGCCAAAG
16122785 ATAGTGTTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (48 bp):
CTTCAAGGACTCATGATCGGTGTGTATGACGAATTCCTTGGGCCAAAG
Found at i:16125617 original size:21 final size:21
Alignment explanation
Indices: 16125591--16125632 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16125581 GAACCCGAGT
*
16125591 CGTTTAGTTCCCGATCGTAAA
1 CGTTTAGTTCCCAATCGTAAA
16125612 CGTTTAGTTCCCAATCGTAAA
1 CGTTTAGTTCCCAATCGTAAA
16125633 AGAAGAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
CGTTTAGTTCCCAATCGTAAA
Found at i:16125797 original size:22 final size:22
Alignment explanation
Indices: 16125767--16125810 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16125757 TTTGGTATTT
16125767 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
* *
16125789 GGGATTTGGTATGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
16125811 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:16126903 original size:10 final size:10
Alignment explanation
Indices: 16126888--16126929 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
16126878 TTTGCAAGTT
16126888 TTGAGCTAAA
1 TTGAGCTAAA
* *
16126898 TTGAGCTGAT
1 TTGAGCTAAA
*
16126908 TTGAGCT-CA
1 TTGAGCTAAA
16126917 TTGAGCTAAA
1 TTGAGCTAAA
16126927 TTG
1 TTG
16126930 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:16137680 original size:50 final size:51
Alignment explanation
Indices: 16137620--16137757 Score: 174
Period size: 50 Copynumber: 2.7 Consensus size: 51
16137610 GGTAAAGAGG
* **
16137620 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATGAG-AGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-GCATGAGTACA
*
16137670 TCACC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGGCATGAGTACA
1 TC-CCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGGCATGAGTACA
* * *
16137721 TCCCATGTAAGGCCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
16137758 TGTTATTATC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
49 1 0.01
50 42 0.55
51 33 0.43
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (51 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGGCATGAGTACA
Found at i:16143403 original size:13 final size:13
Alignment explanation
Indices: 16143385--16143409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16143375 TCCAGCAACA
16143385 ATGAATTTATTTC
1 ATGAATTTATTTC
16143398 ATGAATTTATTT
1 ATGAATTTATTT
16143410 GGTGATGATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:16143568 original size:50 final size:50
Alignment explanation
Indices: 16143509--16143701 Score: 298
Period size: 50 Copynumber: 3.8 Consensus size: 50
16143499 ATTGGGGTAA
16143509 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
16143559 AGAGGTCCCATGTAAGACCATGTCCGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
16143609 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCG-GCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATG
** *
16143659 AGTACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16143702 TGTTATTATC
Statistics
Matches: 130, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 95 0.73
51 34 0.26
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16160007 original size:20 final size:20
Alignment explanation
Indices: 16159982--16160025 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
16159972 GCTAATGGAA
*
16159982 AGCTAAATTGAGCTCGAATG
1 AGCTAAATTGAGCTCAAATG
16160002 AGCTAAATTGAGCTCAAATG
1 AGCTAAATTGAGCTCAAATG
16160022 AGCT
1 AGCT
16160026 GGTTGGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (20 bp):
AGCTAAATTGAGCTCAAATG
Found at i:16175171 original size:12 final size:11
Alignment explanation
Indices: 16175129--16175170 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
16175119 TAGTTTCTCG
*
16175129 AAAAAAAACTC
1 AAAAAAAATTC
16175140 GAAAAAAAATTC
1 -AAAAAAAATTC
16175152 AAAAAAAATTC
1 AAAAAAAATTC
16175163 AAAAAAAA
1 AAAAAAAA
16175171 AACTAGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:16177836 original size:20 final size:20
Alignment explanation
Indices: 16177813--16177859 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
16177803 GGGTTGAGGT
16177813 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
16177833 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
16177853 TGAGCTG
1 TGAGCTG
16177860 GAAGCGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:16188085 original size:15 final size:13
Alignment explanation
Indices: 16188067--16188102 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
16188057 TTTTTCAAAT
16188067 TTTTTTTTCTTTCGA
1 TTTTTTTTC-TT-GA
16188082 TTTTTTTTCTTGA
1 TTTTTTTTCTTGA
16188095 TTTTTTTT
1 TTTTTTTT
16188103 TCGAAACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCTTGA
Found at i:16193411 original size:21 final size:21
Alignment explanation
Indices: 16193385--16193428 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
16193375 NNNNNAAATA
16193385 CCATACCATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
16193406 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
16193427 CC
1 CC
16193429 CAAATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:16216202 original size:15 final size:15
Alignment explanation
Indices: 16216157--16216222 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
16216147 TCACTCAATT
*
16216157 TTTCTTTTTCA-TCTT
1 TTTC-TTTTCATTCTC
*
16216172 TTTCTTTTC-TT-GC
1 TTTCTTTTCATTCTC
16216185 TTTCTTTTCATTCTC
1 TTTCTTTTCATTCTC
* *
16216200 TTT-TTTTGAATTTTC
1 TTTCTTTT-CATTCTC
16216215 TTTCTTTT
1 TTTCTTTT
16216223 TTTCATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.22
14 12 0.29
15 16 0.39
16 4 0.10
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTCTTTTCATTCTC
Found at i:16216220 original size:19 final size:20
Alignment explanation
Indices: 16216171--16216242 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
16216161 TTTTTCATCT
**
16216171 TTTTCTTTTCTTGCTTTC--
1 TTTTCTTTTCTTTTTTTCAA
* *
16216189 TTTTCATTCTCTTTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
16216210 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
16216229 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
16216243 GTATTTTCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 5 0.12
19 25 0.58
20 8 0.19
21 5 0.12
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:16220593 original size:77 final size:76
Alignment explanation
Indices: 16220460--16220607 Score: 203
Period size: 77 Copynumber: 1.9 Consensus size: 76
16220450 AGATCTGATC
* *
16220460 GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGGCAACTCGATCTTGGTTCGCGCGCAA-CCTT
1 GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGACAACTCGATCTTGGTCCGCGCGCAATCC-T
16220524 CTATCACCACGT
65 CTATCACCACGT
* *
16220536 GTCTATAGCTCTCGTTGGA-TTTTC-CTGTGACTTGACAAGCTCGATCTTGGTCCGCGCGCAATC
1 GTCTAGAGCT-TCGTAGGAGTTTTCTC-GTGACTTGACAA-CTCGATCTTGGTCCGCGCGCAATC
16220599 CTCTATCAC
63 CTCTATCAC
16220608 TTCTCTTGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
75 1 0.02
76 25 0.39
77 36 0.56
78 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.32
Consensus pattern (76 bp):
GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGACAACTCGATCTTGGTCCGCGCGCAATCCTC
TATCACCACGT
Found at i:16246770 original size:23 final size:23
Alignment explanation
Indices: 16246738--16246849 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
16246728 CTTTTTGAAC
* *
16246738 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* **
16246761 TATTACCATTTCAAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
16246784 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
16246807 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
16246830 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
16246850 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:16246814 original size:46 final size:46
Alignment explanation
Indices: 16246738--16246849 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
16246728 CTTTTTGAAC
* *
16246738 CATTAACATTTCGTACCAAATCGTATTACCATTTCAAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCAAACCAAATCA
* **
16246784 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCAAACCAAATCA
* *
16246830 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
16246850 CCCAAAACCG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCAAACCAAATCA
Found at i:16247143 original size:19 final size:18
Alignment explanation
Indices: 16247118--16247179 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 18
16247108 TCGTGAATTG
16247118 AAAAAAAAATTCGTGCAA
1 AAAAAAAAATTCGTGCAA
16247136 AGAAAAAAAATTCGTGC--
1 A-AAAAAAAATTCGTGCAA
16247153 AAAAAAAAATTCGTGCATA
1 AAAAAAAAATTCGTGCA-A
16247172 AAAAAAAA
1 AAAAAAAA
16247180 GAGTTTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 15 0.38
17 1 0.03
18 1 0.03
19 23 0.57
ACGTcount: A:0.63, C:0.10, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAAAAAAATTCGTGCAA
Found at i:16247157 original size:16 final size:17
Alignment explanation
Indices: 16247119--16247178 Score: 86
Period size: 16 Copynumber: 3.5 Consensus size: 17
16247109 CGTGAATTGA
16247119 AAAAAAAATTCGTGCAAAG
1 AAAAAAAATTCGTGC--AG
16247138 AAAAAAAATTCGTGCA-
1 AAAAAAAATTCGTGCAG
*
16247154 AAAAAAAATTCGTGCAT
1 AAAAAAAATTCGTGCAG
16247171 AAAAAAAA
1 AAAAAAAA
16247179 AGAGTTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.40
17 9 0.22
19 15 0.38
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.17
Consensus pattern (17 bp):
AAAAAAAATTCGTGCAG
Found at i:16250638 original size:23 final size:23
Alignment explanation
Indices: 16250577--16250638 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
16250567 NNNNNNNNNN
* * **
16250577 ACCAATTCGTACCAAATCGTATT
1 ACCATTTCGTAACAAATCACATT
*
16250600 ACCATTTTG-AACCAAATCACATT
1 ACCATTTCGTAA-CAAATCACATT
16250623 ACCATTTCGTAACAAA
1 ACCATTTCGTAACAAA
16250639 CCCAAAACCG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (23 bp):
ACCATTTCGTAACAAATCACATT
Found at i:16259177 original size:25 final size:25
Alignment explanation
Indices: 16259157--16259207 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16259147 TAAGCTCATT
16259157 TCGAATGAGCTGACTTGAGCTCAAG
1 TCGAATGAGCTGACTTGAGCTCAAG
16259182 TCGAATGAGCTGACTTGAGCTCAAG
1 TCGAATGAGCTGACTTGAGCTCAAG
16259207 T
1 T
16259208 GAGCTGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (25 bp):
TCGAATGAGCTGACTTGAGCTCAAG
Found at i:16259212 original size:20 final size:22
Alignment explanation
Indices: 16259161--16259213 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 22
16259151 CTCATTTCGA
16259161 ATGAGCTGACTTGAGCTCAAGTCG
1 ATGAGCTGACTTGAGCTCAA--CG
16259185 AATGAGCTGACTTGAGCTCAA-G
1 -ATGAGCTGACTTGAGCTCAACG
16259207 -TGAGCTG
1 ATGAGCTG
16259214 GAAACGAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.25
22 1 0.04
25 20 0.71
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (22 bp):
ATGAGCTGACTTGAGCTCAACG
Found at i:16279354 original size:12 final size:12
Alignment explanation
Indices: 16279326--16279365 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
16279316 ACTCGATTTC
*
16279326 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
16279338 CTTTCAATTTCT
1 TTTTCAATCTCT
16279350 TTTTCAATCTCT
1 TTTTCAATCTCT
16279362 TTTT
1 TTTT
16279366 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:16280535 original size:13 final size:13
Alignment explanation
Indices: 16280519--16280557 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
16280509 TGCTCACTTC
16280519 TTTTTTTCGAA--
1 TTTTTTTCGAATT
16280530 TTTTTTTCGAATT
1 TTTTTTTCGAATT
*
16280543 TTTTTTTTGAATT
1 TTTTTTTCGAATT
16280556 TT
1 TT
16280558 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
13 14 0.56
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:16280557 original size:11 final size:11
Alignment explanation
Indices: 16280519--16280547 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16280509 TGCTCACTTC
16280519 TTTTTTTCGAA
1 TTTTTTTCGAA
16280530 TTTTTTTCGAA
1 TTTTTTTCGAA
16280541 TTTTTTT
1 TTTTTTT
16280548 TTTGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:16299118 original size:68 final size:67
Alignment explanation
Indices: 16299019--16299242 Score: 199
Period size: 67 Copynumber: 3.3 Consensus size: 67
16299009 ATAGCCGAGC
* * *
16299019 CATGGTCTTACACAGTCTG-AA-CCCATGTTTAACCTCATAG-CAGACTCTATTGGTTGCCATAG
1 CATGGTCTTACAC-CT-TGTAACCCCATGTTTAACATCAT-GTCAGACTCTATTGGTTACCATAG
* *
16299081 TTGAG
63 CTAAG
** * * *
16299086 TTGTGGTCTTACACCTTGTAACCCCATATTTAACATCCTGTCTGACTCTATTGGTTACCATAGCT
1 -CATGGTCTTACACCTTGTAACCCCATGTTTAACATCATGTCAGACTCTATTGGTTACCATAGCT
16299151 AAG
65 AAG
* * *
16299154 CATGGTCTTACACCTTGTAACCCCATGTTTAACATCCT-TGCGGACTTTATTGGTTA-CATTAGC
1 CATGGTCTTACACCTTGTAACCCCATGTTTAACATCATGT-CAGACTCTATTGGTTACCA-TAGC
*
16299217 CAAG
64 TAAG
* *
16299221 CTAAGGCCTTACACCTTG-AACC
1 C-ATGGTCTTACACCTTGTAACC
16299243 TTTTTTGAGG
Statistics
Matches: 132, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
66 5 0.04
67 65 0.49
68 62 0.47
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (67 bp):
CATGGTCTTACACCTTGTAACCCCATGTTTAACATCATGTCAGACTCTATTGGTTACCATAGCTA
AG
Found at i:16299173 original size:67 final size:67
Alignment explanation
Indices: 16299061--16299242 Score: 208
Period size: 67 Copynumber: 2.7 Consensus size: 67
16299051 CCTCATAGCA
* * * **
16299061 GACTCTATTGGTTGCCATAGTTGAGTTGTGGTCTTACACCTTGTAACCCCATATTTAACATCC-T
1 GACTCTATTGGTTACCATAGCTAAG-CATGGTCTTACACCTTGTAACCCCATATTTAACATCCTT
*
16299125 GTCT
65 G-CG
*
16299129 GACTCTATTGGTTACCATAGCTAAGCATGGTCTTACACCTTGTAACCCCATGTTTAACATCCTTG
1 GACTCTATTGGTTACCATAGCTAAGCATGGTCTTACACCTTGTAACCCCATATTTAACATCCTTG
16299194 CG
66 CG
* * * *
16299196 GACTTTATTGGTTA-CATTAGCCAAGCTAAGGCCTTACACCTTG-AACC
1 GACTCTATTGGTTACCA-TAGCTAAGC-ATGGTCTTACACCTTGTAACC
16299243 TTTTTTGAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 2 0.02
67 60 0.60
68 38 0.38
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (67 bp):
GACTCTATTGGTTACCATAGCTAAGCATGGTCTTACACCTTGTAACCCCATATTTAACATCCTTG
CG
Found at i:16303018 original size:15 final size:16
Alignment explanation
Indices: 16302998--16303030 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16302988 TTTTTCTCTA
16302998 CTTCATT-CAACACAC
1 CTTCATTCCAACACAC
*
16303013 CTTCATTCCCACACAC
1 CTTCATTCCAACACAC
16303029 CT
1 CT
16303031 CTCTCTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (16 bp):
CTTCATTCCAACACAC
Found at i:16305111 original size:59 final size:59
Alignment explanation
Indices: 16305019--16305132 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
16305009 CATTGAGTCA
16305019 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
1 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
* * *
16305078 AATGGCTTAACAGTTTCTCGTAGGGTTCTTGTTGTGATGAGAGGACAAAAAAGGG
1 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGG
16305133 CACTCTACAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.30
Consensus pattern (59 bp):
AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
Found at i:16316535 original size:22 final size:23
Alignment explanation
Indices: 16316510--16316558 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
16316500 TTGCTTGTAC
*
16316510 TTAAGTAAATT-TTGTTA-CATTT
1 TTAAG-AAATTGTGGTTAGCATTT
*
16316532 TTAAGATATTGTGGTTAGCATTT
1 TTAAGAAATTGTGGTTAGCATTT
16316555 TTAA
1 TTAA
16316559 TATGGCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (23 bp):
TTAAGAAATTGTGGTTAGCATTT
Found at i:16319414 original size:21 final size:21
Alignment explanation
Indices: 16319390--16319432 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16319380 CACTTTGGTG
16319390 ATTAAAAATATTTTGATTTTA
1 ATTAAAAATATTTTGATTTTA
*
16319411 ATTAAAAATTTTTTGATTTTA
1 ATTAAAAATATTTTGATTTTA
16319432 A
1 A
16319433 GGAAGCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTAAAAATATTTTGATTTTA
Found at i:16324570 original size:14 final size:14
Alignment explanation
Indices: 16324551--16324583 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16324541 AATGAGTAAT
16324551 TCCACTATATGTAG
1 TCCACTATATGTAG
*
16324565 TCCACTATATTTAG
1 TCCACTATATGTAG
16324579 TCCAC
1 TCCAC
16324584 ACTACAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (14 bp):
TCCACTATATGTAG
Found at i:16334226 original size:20 final size:21
Alignment explanation
Indices: 16334203--16334242 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16334193 GAAGAGTTTC
*
16334203 AGGATAAAAT-GTGTTTTTGT
1 AGGAGAAAATGGTGTTTTTGT
*
16334223 AGGAGAAAGTGGTGTTTTTG
1 AGGAGAAAATGGTGTTTTTG
16334243 AGGGAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.40
Consensus pattern (21 bp):
AGGAGAAAATGGTGTTTTTGT
Found at i:16340455 original size:39 final size:39
Alignment explanation
Indices: 16340394--16340471 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
16340384 GTTGGTTTGC
** * *
16340394 CATATGTTCTTACTTATATAATGATTTGCTACTTTTTTT
1 CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
* *
16340433 CATATGTTCTTAAATATCTAATGTTTTACTACTGTTTTT
1 CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
16340472 AAGTGTAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (39 bp):
CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
Found at i:16340519 original size:108 final size:109
Alignment explanation
Indices: 16340329--16340533 Score: 315
Period size: 108 Copynumber: 1.9 Consensus size: 109
16340319 CTCATTTTAA
* * * *
16340329 GTTCTTAAATATCTACTGTTTGGCTAGTATTTTATAAGTGTTGTTTTGGTTAAGTGTTGGTTTGC
1 GTTCTTAAATATCTAATGTTTGACTACTATTTTATAAGTGTAGTTTTGGTTAAGTGTTGGTTTGC
*
16340394 CATATGTTCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
66 CATATGTCCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
* * *
16340438 GTTCTTAAATATCTAATGTTTTACTACTGTTTT-TAAGTGTAGTTTTGGTTATA-TGTTGGTTTT
1 GTTCTTAAATATCTAATGTTTGACTACTATTTTATAAGTGTAGTTTTGGTTA-AGTGTTGGTTTG
16340501 CCATATGTCCTTACTTATATAATGATTTGCTAC
65 CCATATGTCCTTACTTATATAATGATTTGCTAC
16340534 CATTTTAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 58 0.67
109 29 0.33
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.52
Consensus pattern (109 bp):
GTTCTTAAATATCTAATGTTTGACTACTATTTTATAAGTGTAGTTTTGGTTAAGTGTTGGTTTGC
CATATGTCCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
Found at i:16340658 original size:69 final size:69
Alignment explanation
Indices: 16340579--16340823 Score: 264
Period size: 69 Copynumber: 3.6 Consensus size: 69
16340569 AAAATTTCAC
*
16340579 ATGTTCTTAAATATCTAATATTTTGCTATTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
16340644 TCAT
66 TCAT
* * * * ** * *** *
16340648 ATGTTCTTAAATATCTACT-TTTTGGCTACTGTTTGTAA-AC-TGTTGTAACATATGTCAAAATT
1 ATGTTCTTAAATATCTAATATTTT-GCTACTGTTTTTAAGTCTTGTT-TTAGTTAAGTGTTAGTT
*
16340710 T-TCTT
64 TGTCAT
* * * * *
16340715 ATGTTCTCAAATATCTAATGTTTTGCTACTGTTTCTAAGTCTTGTTTTAGTTGAGTGTTGGTTTG
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
*
16340780 CCAT
66 TCAT
*
16340784 ATGTTCTTAAATATCTAAGATTTTGCTACTGTTTTTAAGT
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGT
16340824 GTAACATACT
Statistics
Matches: 137, Mismatches: 33, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
67 37 0.27
68 28 0.20
69 72 0.53
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.51
Consensus pattern (69 bp):
ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
TCAT
Found at i:16340740 original size:136 final size:136
Alignment explanation
Indices: 16340555--16340817 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 136
16340545 TGTTTTAAAG
* * *
16340555 TGTAACATATGCCAAAAATTTCACATGTTCTTAAATATCTAATATTTTGCTATTGTTTTTAAGTC
1 TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
* *
16340620 TTGTTTTAGTTAAGTGTTAGTTTGTCATATGTTCTTAAATATCT-ACTTTTTGGCTACTGTTTGT
66 TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTT-GCTACTGTTTGT
16340684 AAACTGT
130 AAACTGT
* * ** *
16340691 TGTAACATATGTCAAAATTTTCTTATGTTCTCAAATATCTAATGTTTTGCTACTGTTTCTAAGTC
1 TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
* * *
16340756 TTGTTTTAGTTGAGTGTTGGTTTGCCATATGTTCTTAAATATCTAAGATTTTGCTACTGTTT
66 TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTTGCTACTGTTT
16340818 TTAAGTGTAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
136 108 0.96
137 5 0.04
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (136 bp):
TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTTGCTACTGTTTGTA
AACTGT
Found at i:16343203 original size:2 final size:2
Alignment explanation
Indices: 16343196--16343225 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16343186 AAACATGGAA
16343196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16343226 TTAGGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16343354 original size:24 final size:23
Alignment explanation
Indices: 16343327--16343384 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
16343317 ACATATATAT
16343327 ATATATATATATA-AATAAAAATGC
1 ATATATATATATAGAATAAAAA--C
* *
16343351 ATATAGAT-TATAGAATAATAAC
1 ATATATATATATAGAATAAAAAC
*
16343373 ATATATAAATAT
1 ATATATATATAT
16343385 GTATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 7 0.25
23 7 0.25
24 14 0.50
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATATATATATAGAATAAAAAC
Found at i:16345269 original size:6 final size:6
Alignment explanation
Indices: 16345258--16345293 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
16345248 TTAATGATTT
16345258 AATATA AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA
16345294 TATAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:16345842 original size:16 final size:16
Alignment explanation
Indices: 16345821--16345854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16345811 GACTGTTGAA
*
16345821 CTTCTGCCGCCGCCGC
1 CTTCTGACGCCGCCGC
*
16345837 CTTCTGACGCCGTCGC
1 CTTCTGACGCCGCCGC
16345853 CT
1 CT
16345855 ACCACCACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.50, G:0.24, T:0.24
Consensus pattern (16 bp):
CTTCTGACGCCGCCGC
Found at i:16348398 original size:15 final size:15
Alignment explanation
Indices: 16348378--16348415 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
16348368 TATATACTTG
16348378 TATATATATTTTATA
1 TATATATATTTTATA
16348393 TATATAGT-TTTTATA
1 TATATA-TATTTTATA
*
16348408 TACATATA
1 TATATATA
16348416 CGTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATATATATTTTATA
Found at i:16353223 original size:5 final size:5
Alignment explanation
Indices: 16353206--16353260 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
16353196 GAATGTTAAA
*
16353206 AAAAG AAAA- AAAAG AAAAG -AAA- AAAAG AAAAG AAAAG AAGA- AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
16353252 AAAAG AAAA
1 AAAAG AAAA
16353261 AGTAGAGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 13 0.30
5 31 0.70
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16353230 original size:13 final size:13
Alignment explanation
Indices: 16353203--16353261 Score: 75
Period size: 14 Copynumber: 4.4 Consensus size: 13
16353193 AAAGAATGTT
*
16353203 AAAAAAAGAAAAA
1 AAAAAAAGAAAAG
16353216 AAAGAAAAGAAAA-
1 AAA-AAAAGAAAAG
16353229 AAAGAAAAGAAAAG
1 AAA-AAAAGAAAAG
16353243 AAGAAAAAGAAAAG
1 AA-AAAAAGAAAAG
16353257 AAAAA
1 AAAAA
16353262 GTAGAGGCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
13 19 0.44
14 23 0.53
15 1 0.02
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:16353594 original size:45 final size:45
Alignment explanation
Indices: 16353531--16353617 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
16353521 TTTTATTCGT
* *
16353531 TTTCGTATTTTGGCAAAATATGCCATCTTGATCAATTTATTCTCA
1 TTTCGTATCTTGGAAAAATATGCCATCTTGATCAATTTATTCTCA
* ** *
16353576 TTTCGTATCTTGGAAAAATTTGTTATCTTGATTAATTTATTC
1 TTTCGTATCTTGGAAAAATATGCCATCTTGATCAATTTATTC
16353618 ATTTCGAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.48
Consensus pattern (45 bp):
TTTCGTATCTTGGAAAAATATGCCATCTTGATCAATTTATTCTCA
Found at i:16354708 original size:41 final size:42
Alignment explanation
Indices: 16354650--16354756 Score: 126
Period size: 41 Copynumber: 2.5 Consensus size: 42
16354640 CAAATCGAAT
* * *
16354650 CTTATCTCTCCGGAGTTGCAGTAGAGCAGATT-ATATCAAAC
1 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAATAACAAAC
* *
16354691 CTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAATAACAAAC
1 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--AATAACAAAC
* *
16354735 CTTATCCCTTTGAAGTTGCAGT
1 CTTATCTCTCTGAAGTTGCAGT
16354757 GGGGCAGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 28 0.50
44 28 0.50
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
CTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAATAACAAAC
Found at i:16354766 original size:44 final size:44
Alignment explanation
Indices: 16354663--16354769 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
16354653 ATCTCTCCGG
* * *
16354663 AGTTGCAGTAGAGCAGATT---ATATCAAACCTTATCTCTCTGA
1 AGTTGCAGTAGAGCAGGTTGAAATAACAAACCTTATCCCTCTGA
* *
16354704 AGTTGCAGTAGAGTAGGTTGAAATAACAAACCTTATCCCTTTGA
1 AGTTGCAGTAGAGCAGGTTGAAATAACAAACCTTATCCCTCTGA
* *
16354748 AGTTGCAGTGGGGCAGGTTGAA
1 AGTTGCAGTAGAGCAGGTTGAA
16354770 GATATAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 17 0.31
44 38 0.69
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTTGCAGTAGAGCAGGTTGAAATAACAAACCTTATCCCTCTGA
Done.